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Area of Science:

  • Genomics
  • Neurodevelopmental Disorders
  • Human Genetics

Background:

  • Understanding large-effect pathogenic variation is crucial for autism spectrum disorder (ASD) etiology.
  • Previous studies using short-read sequencing have limitations in detecting complex structural variants (SVs).
  • Phased genome assemblies offer a more comprehensive view of genetic variation.

Purpose of the Study:

  • To characterize de novo mutations, structural variants (SVs), and DNA methylation in individuals with unsolved autism cases using long-read sequencing (LRS).
  • To develop and apply a workflow for prioritizing pathogenic variants by integrating autism risk genes and regulatory elements.
  • To evaluate the utility of phased genomes and pangenome controls for identifying complex mutations.

Main Methods:

  • Generated long-read sequencing (LRS) data for 189 individuals from 51 families with unsolved autism cases.
  • Constructed phased and near-complete genome assemblies.
  • Applied read- and assembly-based strategies for variant characterization, including SVs and DNA methylation, using LRS pangenome controls.

Main Results:

  • Filtered >97% of common SVs using LRS pangenome controls.
  • Observed no increased autosomal SV burden in probands versus siblings, but a trend toward increased X chromosome SV burden in affected females.
  • Identified three pathogenic variants (TBL1XR1, MECP2, SYNGAP1) and nine candidate de novo/biallelic inherited SVs, many missed by short-read sequencing.

Conclusions:

  • Phased genomes are powerful for discovering complex and pathogenic mutations associated with autism.
  • LRS and pangenome approaches significantly enhance the detection of structural variants.
  • The developed prioritization workflow aids in identifying clinically relevant variants for autism.